name about category URL
3dslicer multi-platform, free and open source software package for visualization and medical image computing Graphics https://www.slicer.org
454 sequencing data analysis software Bioinformatics http://454.com
R free software environment for statistical computing and graphics Data Analysis http://www.r-project.org
a2ps any to postscript System Tools http://www.gnu.org/software/a2ps
abaqus finite element analysis Physics http://www.3ds.com
abyss de nono sequence assembler intended for short paired-end reads and large genomes Bioinformatics http://github.com/bcgsc/abyss
adapterremoval rapid adapter trimming, identification, and read merging Bioinformatics http://github.com/MikkelSchubert/adapterremoval
ale Assembly Likelihood Estimator Bioinformatics http://github.com/sc932/ALE
aligngraph Algorithm for secondary de novo genome assembly guided by closely related references Bioinformatics http://github.com/baoe/AlignGraph
allpathslg high quality genome assembly from low cost data Bioinformatics http://broadinstitute.org/software/allpaths-lg/blog
amber assisted model building with energy refinement Molecular Biology http://ambermd.org
amira a powerful, multifaceted 3D software platform for visualizing, manipulating, and understanding biomedical data coming from all types of sources and modalities Graphics http://www.vsg3d.com/amira
anaconda scientific python distribution Programming Tools http://continuum.io
anaconda3 scientific python distribution Programming Tools http://continuum.io
analysis evolutionary genetic analysis Bioinformatics http://molpopgen.org
ant Java Library and Command Line Tool for building packages Programming Tools http://ant.apache.org
ants Advanced Normalization Tools (ANTs) extracts information from complex datasets that include imaging Libraries http://picsl.upenn.edu/software/ants/
arden2bytecode language to represent medical knowledge Bioinformatics http://arden2bytecode.sourceforge.net
arem peak caller for ChIP-Seq experiments that robustly handles short readds with multiple possible mappings Bioinformatics http://sourceforce.net/projects/arem
argparse argparse Libraries http://www.python.org
armadillo C++ linear algebra library Libraries http://arma.sourceforge.net
arpack collection of Fortran77 subroutines designed to solve large scale eigenvalue problems Libraries http://www.caam.rice.edu/software/ARPACK/
arrayfire ArrayFire is a high-performance software library designed for maximum productivity and speed without the hassle of writing difficult low-level device code. Libraries http://arrayfire.com
ase Atomistic Simulation Environment Molecular Biology https://wiki.fysik.dtu.dk/ase/overview.html
aspera high performance file transfer Accessories http://asperasoft.com
astrobear Collection of libraries used by astrobear Libraries http://astrobear.pas.rochester.edu
astropy community python library for astronomy Physics http://www.astropy.org
atk accessibility toolkit Libraries http://ftp.gnome.org/pub/gnome/sources/atk
atlas automatically tuned linear algebra software Mathematics http://sourceforge.net/projects/math-atlas
audacity audio editor Accessories http://audacityteam.org
autoconf generate configure scripts Programming Tools http://www.gnu.org/software/autoconf
autodockvina molecular docking and virtual screening Molecular Biology http://vina.scripps.edu
automake generate Makefile.in files Programming Tools http://www.gnu.org/software/automake
avogadro molecule editor and visualizer Chemistry http://avogadro.cc
bali-phy bayesian alignment and phylogeny estimation Bioinformatics http://www.bali-phy.org
bam2x extract info from bam files Bioinformatics http://github.com/nimezhu/bam2x
bamtools API and command line toolkit for working with BAM data Bioinformatics http://github.com/pezmaster31/bamtools
basespace-cli BaseSpace Sequence Hub Bioinformatics http://basespace.illumina.com
bazel build tool Programming Tools http://bazel.io
bbcp file transfer client Internet http://www.slac.stanford.edu/~abh/bbcp
bbmap BBMap short read aligned and other bioinformatic tools Bioinformatics http://sourceforge.net/projects/bbmap
bcftools program for variant calling and manipulating VCFs and BCFs Bioinformatics https://github.com/samtools/bcftools/wiki
bcl2fastq bcl conversion and multiplexing Bioinformatics http://www.illumina.com
bear2fix Routines for analyzing hdf5 files produced by astrobear Physics http://astrobear.pas.rochester.edu
beast2 Bayesian Evolutionary Analysis by Sampling Trees Bioinformatics http://beast2.org
bedops fast, highly scalable and easily-parallelizable genome analysis toolkit Bioinformatics http://bedops.readthedocs.io
bedtools genome arithmetic suite Bioinformatics http://bedtools.readthedocs.org
bfast Blat-like Fast Accurate Search Tool Bioinformatics http://sourceforge.net/projects/bfast
bioformats Tools for manipulating open microscopy formats Libraries http://openmicroscopy.org
biom-format a general-use format for representing biological sample by observation contingency tables Bioinformatics http://biom-format.org
bioperl Perl code useful in biology Bioinformatics http://www.bioperl.org
biopython tools for biological computation Libraries http://biopython.org
bioxtasraw analysis of small angle x-ray scattering data Chemistry http://sourceforge.net/projects/bioxtasraw/b1
bismark bisulfite read mapper and methylation caller Bioinformatics http://www.bioinformatics.babraham.ac.uk/projects/bismark
bison General-purpose parser generator Libraries http://www.gnu.org/software/bison/
blas Basic Linear Algebra Subprograms Libraries http://www.netlib.org/blas/
blasr PacBio long read aligner Bioinformatics http://github.com/PacificBiosciences/blasr
blast basic local alignment search tool Bioinformatics http://blast.ncbi.nlm.nih.gov
blat BLAST-like alignment tool Bioinformatics http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/blat/
bonnie benchmark suite System Tools http://coker.com.au/bonnie++
boost portable C++ source libraries Libraries http://www.boost.org
bowtie ultrafast memory-efficient short read aligner Bioinformatics http://bowtie-bio.sourceforge.net
bowtie2 ultrafast memory-efficient short read aligner Bioinformatics http://bowtie-bio.sourceforge.net/bowtie2
bwa Burrows-Wheeler aligner Bioinformatics http://bio-bwa.sourceforge.net
bwidget TCL widget library Programming Tools http://core.tcl.tk/bwidget
bwtool command-line utility for bigWig files Bioinformatics http://github.com/CRG-Barcelona/bwtool
bzip2 compression System Tools http://bzip.org
caffe deep learning framework Computer Science http://caffe.berkeleyvision.org
cairo 2D graphics library with support for multiple output devices Libraries http://cairographics.org
canu fork of Celera Assembler, designed for high-noise single-molecule sequencing Bioinformatics http://github.com/marbl/canu
catdoc read MS Word and Excel files Accessories http://www.wagner.pp.ru/~vitus/software/catdoc
cdec decoder, aligner, and learning framework for statistical machine translation and similar prediction models Computer Science http://cdec-decoder.org
cdo Climate Data Operators Physics http://code.zmaw.de/projects/cdo
ceas cis-regulatory element annotation system Bioinformatics http://liulab.dfci.harvard.edu/CEAS
cgal Computational Geometry Algorithms Library Libraries http://www.cgal.org
chimera visualization of molecular structures Chemistry http://www.cgl.ucsf.edu/chimera
circos circular genome variation and data visualization tool Graphics http://circos.ca
cisa contig integrator for sequence assembly Bioinformatics http://sb.nhri.org.tw/CISA
cistrome platform for transcriptional regulation studies Bioinformatics http://bitbucket.org/cistrome/cistrome-applications-harvard/src
clapack f2c'd version of LAPACK Libraries http://www.netlib.org/clapack
clustalw multiple sequence alignment Bioinformatics http://clustal.org
clustalx multiple sequence alignment Bioinformatics http://clustal.org
cmake an extensible, open-source system that manages the build process in an operating system System Tools http://www.cmake.org
commet COmpare Multiple METagenomes Bioinformatics http://colibread.inria.fr/software/commet
comsol multiphysics simulation Physics http://www.comsol.com
conifer copy number inference from exome reads Bioinformatics http://conifer.sourceforge.net
convert ImageMagick Convert utility System Tools http://www.imagemagick.org
corset clustering de novo assembled transcripts and counting overlapping reads Bioinformatics http://github.com/Oshlack/Corset
cp2k program to perform atomistic and molecular simulations of solid state, liquid, molecular, and biological systems Chemistry http://www.cp2k.org
cpc Coding Potential Calculator Bioinformatics http://cpc.cbi.pku.edu.cn
cpmd Car-Parrinello Molecular Dynamics Chemistry http://www.cpmd.org
crisp code for multi-sample variant calling from sequence data Bioinformatics http://github.com/vibansal/crisp
crispresso analysis of CRISPR-Cas9 genome editing outcomes from sequencing data Bioinformatics http://github.com/lucapinello/CRISPResso
ctm C implementation of the correlated topic model (CTM) Mathematics http://www.cs.princeton.edu/~blei/ctm-c/
cuda CUDA Software Development Kit (gcc 4.4.7) Programming Tools https://developer.nvidia.com/cuda-zone
cudamat Python module for performing basic dense linear algebra computations on the CPU using CUDA Libraries http://github.com/cudamat/cudamat
cudnn GPU-accelerated library for deep neural networks Programming Tools http://nvidia.com
cufflinks transcript assembly, differential expression, and differential regulation for RNA-Seq Bioinformatics http://cufflinks.cbcb.umd.edu
curl multiprotocol file transfer library Internet http://curl.haxx.se/libcurl
cushaw gapped short-read alignment Bioinformatics http://cushaw3.sourceforge.net
cutadapt removes adapter sequences from DNA sequencing reads Bioinformatics http://github.com/marcelm/cutadapt
cytoscape network visualization Graphics http://www.cytoscape.org
db Berkeley DB Libraries http://www.oracle.com/technetwork/database/database-technologies/berkeleydb/overview/index.html
dbg2olc assembly of large genomes using long erroneous reads of the third generation sequencing technologies Bioinformatics http://github.com/yechengxi/DBG2OLC
dcs client application designed to be run locally on a data producer's machine System Tools http://scm.dataconservancy.org
ddimap DDiMap Bioinformatics https://github.com/jpspence/DDiMAPpublic
dealii open source finite element library Libraries http://dealii.org
dendropy phylogenetic computing Bioinformatics http://pythonhosted.org/DendroPy
device advanced, finite element multiphysics simulation environment Physics http://www.lumerical.com
dftb fast approximate DFT for molecules Chemistry http://www.scm.com
diffsplice genome-wide detection of differential splicing events with RNA-seq Bioinformatics http://www.netlab.uky.edu/p/bioinfo/DiffSplice
disperse Automatic identification of persistent structures Mathematics http://www2.iap.fr/users/sousbie/web/html/indexd41d.html?
dock molecular docking Chemistry http://dock.compbio.ucsf.edu
dofe distribution of fitness effects and rates of adaptive substitution Bioinformatics http://www.lifesci.susx.ac.uk/home/Adam_Eyre-Walker/Website/Software.html
dptools Processing and converting data related to the DFTB+ package Chemistry http://www.dftb-plus.info/tools/dptools
drmaa-slurm DRMAA for Slurm Libraries http://apps.man.poznan.pl/trac/slurm-drmaa
duc File usage analyzer System Tools https://duc.zevv.nl
ea-utils Command-line tools for processing biological sequencing data Libraries https://code.google.com/p/ea-utils/
eclipse integrated development environment Programming Tools http://eclipse.org
eigen C++ template library for linear algebra Libraries http://eigen.tuxfamily.org
elan annotations on video and audio resources Computer Science http://tla.mpi.nl/tools/tla-tools/elan
emacs extensible, customizable text editor Accessories http://www.gnu.org/software/emacs
emboss European Molecular Biology Open Software Suite Bioinformatics http://emboss.sourceforge.net
ensembl-tools variant effect predictor Bioinformatics http://useast.ensembl.org
epstool Epstool is a utility to create or extract preview images in EPS files, fix bounding boxes and convert to bitmaps Accessories http://pages.cs.wisc.edu/~ghost/gsview/epstool.htm
exabayes bayesian tree inference Bioinformatics http://sco.h-its.org/exelixis/web/software/exabayes
examl Exascale Maximum Likelihood (ExaML) code for phylogenetic inference using MPI Bioinformatics http://github.com/stamatak/ExaML
exonerate a generic tool for pairwise sequence comparison Libraries http://www.ebi.ac.uk/~guy/exonerate/
expect automate interactive applications System Tools http://expect.sourceforge.net
express streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences Bioinformatics http://bio.math.berkeley.edu/eXpress/overview.html
falcon experimental PacBio diploid assembler Bioinformatics http://github.com/PacificBiosciences/falcon
fastqc quality control tool for high throughput sequence data Bioinformatics http://www.bioinformatics.babraham.ac.uk/projects/fastqc
fastx FASTQ/A short-reads pre-processing tools Bioinformatics http://hannlab.cshl.edu/fastx_toolkit
fdtd-solutions Single and multi-processor finite-difference time-domain optical design Physics http://www.lumerical.com
fenics solution of differential equations Mathematics http://fenicsproject.org
ferret visualization and analysis environment for studying climate Graphics http://ferret.pmel.noaa.gov
ffi portable, high level programming interface to various calling conventions Libraries http://sourceware.org/libffi
ffmpeg A complete, cross-platform solution to record, convert and stream audio and video Graphics http://www.ffmpeg.org
fftw2 FFTW library for computing the discrete Fourier transform (DFT) Libraries http://www.fftw.org/
fftw3 FFTW3 library for computing the discrete Fourier transform (DFT) Libraries http://www.fftw.org/
fiji Fiji is just ImageJ with plugins Graphics http://fiji.sc
findutils basic directory searchiing utilities System Tools http://gnu.org/software/findutils
firefox web browser Internet http://www.mozilla.org/Firefox
flash merge mates from fragments that are shorter than twice the read length Bioinformatics http://sourceforge.net/projects/flashpage
flens flexible library for efficient numerical solutions Mathematics http://flens.sourceforge.net
flex the fast lexical analyser Libraries http://sourceforge.net/projects/flex/
flowgate free software environment for statistical computing and graphics Data Analysis http://www.r-project.org
fltk a cross-platform C++ GUI toolkit Libraries http://www.fltk.org
freebayes Bayesian haplotype-based polymorphism discovery and genotyping Bioinformatics http://github.com/ekg/freebayes
freeglut OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library Libraries http://freeglut.sourceforge.net
freesurfer processing and analyzing brain MRI images Graphics http://surfer.nmr.mgh.harvard.edu
freetype freely available software library to render fonts Libraries http://www.freetype.org
freexl library to extract valid data from within an Excel spreadsheet Libraries http://www.gaia-gis.it/fossil/freexl/index
fsl analysis tools for FMRI, MRI, and DTI brain imaging data Bioinformatics http://fsl.fmrib.ox.ac.uk
gam-ngs genomic assemblies merger for NGS Bioinformatics http://github.com/vice87/gam-ngs
gamess general atomic and molecular electronic structure system Chemistry http://www.msg.ameslab.gov/gamess
gap2seq filling gaps in scaffolds produced by genome assembly tools Bioinformatics http://www.cs.helsinki.fi/u/lmsalmel/Gap2Seq
gapfiller close gaps produced by a scaffolding program using one or more mate pairs or paired-end libraries Bioinformatics http://baseclear.com
gatb Genome Assembly Tool Box Bioinformatics http://gatb-core.gforge.inria.fr
gatk genome analysis toolkit Bioinformatics http://www.broadinstitute.org/gatk
gaussian quantum chemistry Chemistry http://www.gaussian.com
gcc GNU compiler collection Programming Tools http://gcc.gnu.org
gcta genome-wide complex trait analysis Bioinformatics http://cnsgenomics.com
gdal translator library for raster and vector geospatial data formats Physics http://www.gdal.org
gdc-client GDC data transfer tool Accessories http://github.com/NCI-GDC/gdc-client
gdk-pixbuf toolkit for image loading and pixel buffer manipulation Libraries http://ftp.gnome.org/pub/gnome/
gem5 modular platform for computer system architecture research Programming Tools http://www.gem5.org
geneious bioinformatics tools Bioinformatics http://geneious.com
genepattern computational biology open-source package Bioinformatics http://www.genepattern.org
genetorrent downloading sequence data Bioinformatics http://www.cghub.ucsc.edu/software
genometools open source genome analysis software Bioinformatics http://genometools.org
geos geometry engine, open source Graphics http://trac.osgeo.org/geos
gephi open graph viz platform Graphics http://gephi.github.io
gffcompare classify, merge, tracking, and annotation of GFF files by comparing to a reference annotation GFF Bioinformatics http://github.com/gpertea/gffcompare
gflags command line flags processing Programming Tools http://github.com/gflags
ghc Glasgow Haskell Compiler Programming Tools http://www.haskell.org/haskellwiki/GHC
ghostscript Interpreter for the PostScript language and for PDF Graphics http://www.ghostscript.com
git distributed version control system Programming Tools http://git-scm.com
git-lfs Git large file storage Programming Tools http://git-lfs.github.com
gl2ps an OpenGL to PostScript printing library Libraries http://www.geuz.org/gl2ps/
glew OpenGL Extension Wrangler Library Libraries http://glew.sourceforge.net
glfw free, Open Source, multi-platform library for creating windows with OpenGL or OpenGL ES contexts and receiving many kinds of input Libraries http://www.glfw.org
glib a low-level libraries useful for providing data structure handling for C Libraries http://www.linuxfromscratch.org/blfs/view/svn/general/glib2.html
glibc GNU C library Libraries http://www.gnu.org/s/libc
glog google logging module Programming Tools http://github.com/glog
glpk GNU Linear Programming Kit Libraries http://www.gnu.org/software/glpk/
gmap a genomic mapping and alignment program for mRNA and EST sequences Bioinformatics http://research-pub.gene.com/gmap
gmp GNU Multiple Precision Arithmetic Library Libraries http://gmplib.org
gmt Generic Mapping Tools: open source collection of about 80 command-line tools for manipulating geographic and Cartesian data sets Physics http://gmt.soest.hawaii.edu
gnat GNU Ada compiler Programming Tools http://libre.adacore.com
gnumpy Python interface to GPUs and numpy Libraries http://www.cs.toronto.edu/~tijmen/gnumpy.html
gnuplot plotting program Graphics http://www.gnuplot.info
gnutls secure communications library implementing the SSL, TLS and DTLS protocols and technologies around them Libraries http://gnutls.org
gobject-instrospection middleware layer between C libraries (using GObject) and language bindings Libraries https://wiki.gnome.org/action/show/Projects/GObjectIntrospection
gpaw density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) method and the atomic simulation environment (ASE) Molecular Biology https://wiki.fysik.dtu.dk/gpaw
gperf perfect hash function generator System Tools http://www.gnu.org/software/gperf/
gpfw free, Open Source, multi-platform library for creating windows with OpenGL or OpenGL ES contexts and receiving many kinds of input Libraries http://www.glfw.org
grace WYSIWYG 2D plotting tool Graphics http://plasma-gate.weizmann.ac.il/Grace
graphiz open source graph visualization software Graphics http://www.graphviz.org/
graphlan circular representations of taxonomic and phylogenetic trees Bioinformatics http://bitbucket.org/nsegata/graphlan
gromacs molecular dynamics Molecular Biology http://www.gromacs.org
gshrimp image processing Data Analysis http://people.physics.illinois.edu/Selvin/PRS/students/group.html
gsl GNU scientific library Libraries http://www.gnu.org/s/gsl
gstreamer library for constructing graphs of media-handling components Libraries http://gstreamer.freedesktop.org/
gstreamer-plugins gstreamer Libraries http://notavailable.com
gtk Gimp Toolkit:A multi-platform toolkit for creating graphical user interfaces Libraries http://www.gtk.org
guile GNU Ubiquitous Intelligent Language for Extensions Programming Tools http://www.gnu.org/software/guile/
gurobi optimizer Mathematics http://www.gurobi.com
h5py HDF5 for Python Libraries http://www.h5py.org
h5utils set of utilities for visualization and conversion of scientific data in the free, portable HDF5 format Libraries http://ab-initio.mit.edu/wiki/index.php/H5utils
hal hierarchical alignment format Bioinformatics http://github.com/glennhickey/hal
harfbuzz an OpenType text shaping engine Libraries http://www.freedesktop.org/software/harfbuzz/release/harfbuzz-0.9.27.tar.bz2
harminv a free program (and accompanying library) to solve the problem of harmonic inversion Mathematics http://ab-initio.mit.edu/wiki/index.php/Harminv
hdf4 a library and multi-object file format for storing and managing data between machines Libraries http://www.hdfgroup.org/products/hdf4/
hdf5 data model, library, file format Libraries http://www.hdfgroup.org
hdfview HDF file viewer System Tools http://www.hdfgroup.org/products/java/release/download.html
hg Mercurial Revision Control System System Tools http://mercurial.selenic.com
hisat graph-based alignment of next generation sequencing reads to a population of genomes Bioinformatics http://ccb.jhu.edu/software/hisat2
hmmer biosequence analysis using profile hidden Markov models Bioinformatics http://hmmer.org
homer motif discovery and next-gen sequencing analysis Bioinformatics http://homer.salk.edu
hoomd General purpose particle simulation toolkit Libraries http://codeblue.umich.edu/hoomd-blue
hpctoolkit High performance computing toolkit Programming Tools http://hpctoolkit.org
hpctraceviewer GUI for hpctoolkit Programming Tools http://hpctoolkit.org
hpcviewer GUI for hpctoolkit Programming Tools http://hpctoolkit.org
htseq analysis of high-throughput sequencing data Bioinformatics http://www-huber/embl.de/users/anders/HTseq/doc/overview.html
htslib library for reading/writing high-throughput sequencing data Bioinformatics http://www.htslib.org
hyphy hypothesis testing using phylogenies Bioinformatics http://github.com/veg/hyphy
hypre a library for solving large, sparse linear systems of equations on massively parallel computers Libraries http://computation.llnl.gov/casc/hypre/software.html
idl scientific programming language Data Analysis http://exelisvis.com
idp isoform detection and prediction Bioinformatics http://www.healthcare.uiowa.edu/labs/au/IDP
igv integrative genomics viewer Bioinformatics http://www.broadinstitute.org/igv
ilmbase Industrial Light & Magic base libraries Libraries http://www.openexr.com
imagemagick image processing Libraries http://imagemagick.org
impi Intel MPI Programming Tools http://software.intel.com/en-us/intel-compilers
impute genotype imputation and haplotype phasing Bioinformatics http://mathgen.stats.ox.ac.uk/impute/impute_v2.html
imsl mathematical and statistical functions Libraries http://www.roguewave.com
infernal Infernal (INFERence of RNA ALignment) is for searching DNA sequence databases for RNA structure and sequence similarities Bioinformatics http://infernal.janelia.org
inkscape A powerful, free design tool Graphics http://inkspace.org
intel Intel utilities Programming Tools http://software.intel.com/en-us/intel-compilers
intelpython intel python Programming Tools http://software.intel.com/en-us/intel-compilers
intelpython3 intel python Programming Tools http://software.intel.com/en-us/intel-compilers
iozone filesystem benchmarking System Tools http://iozone.org
ipm integrated performance modeling Programming Tools http://ipm-hpc.sourceforge.net
ipython Interactive Python Programming Tools http://www.python.org
iqtree phylogenomics by maximum likelihood Bioinformatics http://iqtree.org
itk open-source, cross-platform system that provides developers with an extensive suite of software tools for image analysis Libraries http://itk.org
j3d java 3D library Libraries http://java3d.java.net
jags Just Another Gibbs Sampler Data Analysis http://mcmc-jags.sourceforge.net
jamg just annotate my genome Bioinformatics http://jamg.sourceforge.net
japsa Just Another JAva Package for Sequence Analysis Bioinformatics http://github.com/mdcao/japsa
jasper Open source JPEG-2000 part 1 codec Graphics http://www.ece.uvic.ca/~frodo/jasper/
java Java pre-release development kit Programming Tools http://www.java.com
jdk Java development kit Programming Tools http://www.java.com
jellyfish fast parallel k-mer counting for DNA Bioinformatics http://www.cbcb.umd.edu/software/jellyfish
jmol Java viewer for chemical structures in 3D Chemistry http://jmol.org
jpeg free library for JPEG image compression Libraries http://www.ijg.org/
jre Java pre-release development kit Programming Tools http://www.java.com
jruby ruby programming language on the Java virtual machine Programming Tools http://jruby.org
julia high-level, high-performance dynamic programming language Programming Tools http://julialang.org
jupyter Interactive Python Programming Tools http://www.python.org
jupyterhub multiuser version of the notebook designed for centralized deployments in companies, university classrooms and research labs Programming Tools https://github.com/jupyterhub/jupyterhub
kallisto program for quantifying abundances of transcripts from RNA-Seq data Bioinformatics http://pachterlab.github.io/kallisto
karect KAUST assembly read error correction tool Bioinformatics http://github.com/aminallam/karect
kenlm estimates, filters, and queries language models Libraries https://kheafield.com/code/kenlm/
khmer nucleotide sequence k-mer counting, filtering, graph traversal Bioinformatics http://github.com/dib-lab/khmer
lammps molecular dynamics Chemistry http://lammps.sandia.gov
lapack linear algebra package Libraries http://www.netlib.org/lapack
last genome-scale sequence comparison Bioinformatics http://last.cbrc.jp
latex2html bringing high quality documents to the web Accessories http://www.latex2html.org
lcms littlc cms color engine Libraries https://sourceforge.net/projects/lcms/files/
leveldb lightweight single purpose library for persistence with bindings Data Analysis http://leveldb.org
lftp sophisticated ftp/http client, and a file transfer program supporting a number of network protocols System Tools http://lftp.yar.ru
libav a friendly and community-driven effort to provide its users with a set of portable, functional and high-performance libraries for dealing with multimedia formats of all sorts Libraries https://libav.org/download.html
libcanberra implementation of the XDG Sound Theme and Name Specifications, for generating event sounds on free desktops, such as GNOME Libraries http://0pointer.de/lennart/projects/libcanberra/
libctl Guile-based library implementing flexible control files for scientific simulations Libraries http://ab-initio.mit.edu/wiki/index.php/Libctl
libevent The libevent API provides a mechanism to execute a callback function when a specific event occurs on a file descriptor or after a timeout has been reached Libraries http://libevent.org
libffi Foreign Function Interface Libraries http://sourceware.org/libffi
libgd open source code library for the dynamic creation of images by programmers Libraries http://libgd.bitbucket.org
libglew The OpenGL Extension Wrangler Library Libraries http://glew.sourceforge.net
libgpuarray library to manipulate tensors on the GPU Libraries http://github.com/Theano/libgpuarray
libjpeg-turbo JPEG image codec that uses SIMD instructions to accelerate baseline JPEG compression and decompression Libraries http://sourceforge.net/projects/libjpeg-turbo/files/1.3.1/
libogg a multimedia container format, and the native file and stream format for the Xiph.org multimedia codecs Libraries https://www.xiph.org/downloads/
libpng the free reference library for reading and writing PNGs Libraries http://www.libpng.org
libreoffice free office suite Accessories http://libreoffice.org
libsequence C++ class library for evolutionary genetic analysis Bioinformatics http://github.com/molpopgen/libsequence
libsndfile library for reading files containing sampled sound Libraries http://www.mega-nerd.com/libsndfile
libtasn1 ASN.1 library used by GnuTLS, GNU Shishi Libraries http://ftp.gnu.org/gnu/libtasn1/
libtool The GNU Portable Library Tool Libraries http://www.gnu.org/software/libtool/libtool.html
libunwind unwinding library Programming Tools http://github.com/pathscale/libunwind
libvorbis reference implementation of the Vorbis codec Libraries https://www.xiph.org/downloads/
libxc exchange-correlation functionals for density functional theory Chemistry http://www.tddft.org/programs/octopus/wiki/index.php/Libxc
libzip C library for reading, creating, and modifying zip archives Libraries http://www.nih.at/libzip
liggghts discrete element method particle simulation code Physics http://cfdem.com
links long interval nucleotide K-mer scaffolder Bioinformatics http://github.com/warrenlr/LINKS
lmdb lightning memory-mapped database manager Data Analysis http://lmdb.tech
locarna global and local alignment of RNA Bioinformatics http://www.bioinf.uni-freiburg.de/Software/LocARNA
loos lightweight object-oriented structure library Molecular Biology http://loos.sourceforge.net
lordec hybrid error correction program for long PacBio reads Bioinformatics http://atgc-montpellier.fr/lordec
lpp pre- and post-processing capability for the LAMMPS molecular dynamics package Physics http://www.cs.sandia.gov/~sjplimp/lammps.html
lsc long range error correction tool Bioinformatics http://www.healthcare.uiowa.edu/labs/au/LSC
luajit just-in-time compiler for lua Programming Tools http://luajit.org
lxtask Lightweight X Task manager System Tools http://sourceforge.net/projects/lxde/files/LXTask
m4 Unix Macro Processor Libraries https://www.gnu.org/software/m4/
macs model-based analysis for ChIP-Seq Bioinformatics http://liulab.dfci.harvard.edu/MACS
magma GPU accelerated linear algebra Libraries http://developer.nvidia.com/magma
magmaca MAGMA computer algebra system Mathematics http://magma.maths.usyd.edu.au
maker genome annotation pipeline Bioinformatics http://www.yandell-lab.org/software/maker.html
marginalign UCSC Nanopore Bioinformatics http://github.com/benedictpaten/marginAlign
masurca whole genome assembly Bioinformatics http://www.genome.umd.edu/masurca.html
mathematica computation, symbolic mathematics, and visualization Mathematics http://www.wolfram.com
matlab MATLAB (matrix laboratory) is a multi-paradigm numerical computing environment and fourth-generation programming language Mathematics http://www.mathworks.com/products/matlab/
matlab-runtime matlab runtime environment Mathematics http://www.mathworks.com
matplotlib python 2D plotting library Libraries http://matplotlib.org
mc Midnight Commander System Tools http://midnight-commander.org
md5deep compute checksums on arbitrary number of files Accessories http://md5deep.sourceforge.net
mdbtools work with files from Microsoft Access Libraries http://mdbtools.sourceforge.net
meep a free finite-difference time-domain (FDTD) simulation software package developed at MIT to model electromagnetic systems Physics http://ab-initio.mit.edu/wiki/index.php/Meep
megahit ultra-fast single-node solution for large and complex metagenomics assembly Bioinformatics http://github.com/voutcn/megahit
meld visual diff and merge tool Programming Tools http://meldmerge.org
meme fast parallel k-mer counting for DNA Bioinformatics http://www.cbcb.umd.edu/software/jellyfish
mesa 3D graphics library Libraries http://mesa3d.org
metabat tool for accurately reconstructing single genomes from complex microbial communities Bioinformatics http://bitbucket.org/berkeleylab/metabat
mfold RNA secondary structure prediction Molecular Biology http://mfold.rna.albany.edu
mgiza A word alignment tool based on famous GIZA++, extended to support multi-threading, resume training and incremental training Computer Science https://github.com/moses-smt/mgiza
mgltools Molecular Graphics Library Tools Molecular Biology http://mgltools.scripps.edu
mgtaxa taxonomic classification of metagenomic sequences with machine learning Bioinformatics http://andreyto.github.io/mgtaxa
miniasm ultrafast de novo assembly for long noisy reads (though having no consensus step) Bioinformatics http://github.com/lh3/miniasm
minimap experimental tool to find approximate mapping positions between long sequences Bioinformatics http://github.com/lh3/minimap
misopy mixture of isoforms module for isoform quantification using RNA-Seq Bioinformatics http://pypi.pyhon/org/pypi/misopy
mitoprot prediction of mitochondrial targeting sequences Bioinformatics http://ihg.gsf.de/ihg/mitoprot.html
molcas ab initio quantum chemistry software package Chemistry http://www.molcas.org
molden pre and post processing program for molecular and electronic structure Chemistry http://www.cmbi.ru.nl/molden
molstat a collection of tools for simulating and understanding single molecule behavior Chemistry http://bitbucket.org/mgreuter/molstat
mongodb cross-platform document-oriented NoSQL database Data Analysis http://www.mongodb.org
moose multiphysics object-oriented simulation environment Physics http://mooseframework.com
mopac semiempirical quantum chemistry Chemistry http://openmopac.net
mosh remote terminal application allowing roaming, intermittent connectivity, local echo Internet http://mosh.mit.edu
mpb MIT photonic bands Physics http://ab-initio.mit.edu/wiki/index.php/MIT_Photonic_Bands
mpc C library for the arithmetic of complex numbers with arbitrarily high precision and correct rounding of the result Libraries http://www.multiprecision.org
mpfr multiple precision floating point library Libraries http://www.mpfr.org
mpiblast freely available, open- Libraries http://www.mpiblast.org/
mpich high performance and widely portably implementation of the Message Passing Interface standard Programming Tools http://www.mpich.org
mpip lightweight, scalable MPI profiling Programming Tools http://ipm-hpc.sourceforge.net
mplus latent variable modeling program Data Analysis http://statmodel.com
mrbayes bayesian inference of phylogeny Bioinformatics http://mrbayes.sourceforge.net
multiqc aggregate results from bioinformatics analyses across many samples into a single report Bioinformatics http://github.com/ewels/MultiQC
mummer modular system for rapid whole genome alignment of finished or draft sequence Bioinformatics http://sourceforge.net/projects/mummer
muscle multiple sequence alignment Bioinformatics http://www.drive5.com/muscle
mysql open source relational database management system Data Analysis http://www.mysql.com
mysql-python interface for connecting to a MySQL database server from Python Libraries http://sourceforge.net/projects/mysql-python/
mysql-workbench integrated tools environment for MySQL Data Analysis http://dev.mysql.com
namd scalable molecular dynamics Molecular Biology http://www.ks.uiuc.edu/Research/namd
nanocorr error correction for Oxford Nanopore data Bioinformatics http://github.com/jgurtowski/nanocorr
nanopolish Signal-level algorithms for MinION data Bioinformatics http://github.com/jts/nanopolish
nas hybrid approach to take advantage of data generated using MinION device Bioinformatics http://github.com/institut-de-genomique/NaS
ncftp FTP client System Tools http://ncftp.com
ncl NCAR command language Physics http://ncl.ucar.edu
nco NetCDF command operators Programming Tools http://nco.sourceforge.net
netcdf software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data Libraries http://www.unidata.ucar.edu/netcdf
netcdf-fortran software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data Libraries http://www.unidata.ucar.edu/netcdf
netlogo multi-agent programmable modeling environment Programming Tools http://ccl.northwestern.edu/netlogo
nettle cryptographic library that is designed to fit easily in more or less any context Libraries https://ftp.gnu.org/gnu/nettle/
nlopt nonlinear optimization Libraries http://ab-initio.mit.edu/wiki/index.php/NLopt
nodejs Event-driven I/O server-side JavaScript environment based on V8 System Tools http://nodejs.org
novocraft aligner for single-end and paired-end reads Bioinformatics http://www.novocraft.org
numpy fundamental package for scientific computing with Python Libraries http://www.numpy.org/
nupic hierarchical temporary memory Data Analysis http://numenta.org
nwchem quantum chemistry Chemistry http://www.nwchem-sw.org
ocaml OCAML programming language Programming Tools http://ocaml.org
ocproxy OpenConnect proxy Internet http://github.com/cernekee/ocproxy
octave high-level interpreted language, primarily intended for numerical computations Mathematics https://www.gnu.org/software/octave/
octopus density functional theory Chemistry http://www.tddft.org/programs/octopus/wiki/index.php/Main_Page
omero OMERO is client-server software for visualization, management and analysis of biological microscope images. Microscopy https://www.openmicroscopy.org/site/products/omero
opacplot python package for manipulating Equation of State and Opacity data Chemistry http://github.com/tzeferacos/opacplot_deprecated
openbabel chemical toolbox Chemistry http://openbabel.org
openblas optimized BLAS library Libraries http://openblas.net
opencl opencl headers Libraries http://khronos.org
openconnect VPN client Internet http://www.infradead.org/openconnect
opencv Open Source Computer Vision Library Libraries http://opencv.org
openexr High dynamic-range image file format Graphics http://www.openexr.com
openmpi high performance message passing library Programming Tools http://www.openmpi.org
openms LC/MS data management and analyses Chemistry http://open-ms.sourceforge.net
opera optimal genome scaffolding program Bioinformatics http://sourceforge.net/projects/operasf
orca quantum chemistry Chemistry http://www.thch.uni-bonn.de/tc/orca
orthodb database of orthologs Bioinformatics http://orthodb.org
orthomcl ortholog groups of protein sequences Bioinformatics http://orthomcl.org
ortools Google's software suite for combinatorial optimization Libraries http://developers.google.com/optimizations
ovito scientific visualization and analysis software for atomistic simulation data Graphics http://ovito.org
p3dfft parallel three-dimensional fast Fourier transforms Libraries http://code.google.com/p/p3dfft
p4est Parallel AMR on forests of octrees Libraries http://p4est.org
p7zip file archiver System Tools http://p7zip.sourceforge.net
packmol packing optimization for molecular dynamics simulations Chemistry http://www.ime.unicamp.br/~martinez/packmol
paml phylogenetic analysis by maximum likelihood Bioinformatics http://abacus.gene.ucl.ac.uk
pamlx phylogenetic analysis by maximum likelihood Bioinformatics http://abacus.gene.ucl.ac.uk/software/paml.html
pandoc universal document converter Accessories http://pandoc.org
pango library for laying out and rendering of text, with an emphasis on internationalization Libraries http://www.pango.org
parallel shell tool for executing jobs in parallel System Tools http://www.gnu.org/software/parallel
paraview an open-source, multi-platform data analysis and visualization application Graphics http://www.paraview.org
pbcore Python APIs for interacting with PacBio data files Bioinformatics http://github.com/PacificBiosciences/pbcore
pbh5tools swiss-army knife for interrogating PacBio HDF5 files Bioinformatics http://github.com/PacificBiosciences/pbh5tools
pbsuite automated pipeline to align long sequencing reads to high-confidence draft assembles Bioinformatics http://sourceforge.net/p/pb-jelly
pccalc calculates principal components for datasets with large sample sizes Bioinformatics http://ccge.medschl.cam.ac.uk/software/pccalc
pcre Perl Compatible Regular Expressions Libraries http://www.pcre.org
pdbdagcon sequence consensus Bioinformatics http://github.com/PacificBiosciences/pbdagcon
peaksplitter subdivision of ChIP-seq/ChIP-chip regions into discrete signal peaks Bioinformatics http://www.ebi.ac.uk/research/bertone/software
pear Illumina paired-end read and merger Bioinformatics http://sco.h-its.org/exelixis/web/software/pear
pecnv C++ tools for calling structural variants from PE mapping of short reads Bioinformatics http://github.com/molpopgen/pecnv
perf profiling with performance counters Programming Tools http://perf.wiki.kernel.org
perl Perl programming language Programming Tools http://www.perl.org
perl-modules perl modules Libraries http://www.cpan.org
petsc portable, extensible toolkit for scientific computation Mathematics http://www.mcs.anl.gov/petsc
petsc4py PETSc for python Mathematics http://pypi.python.org/pypi/petsc4py
pgplot plotting library for fortran (gfortran 5.2.0) Libraries http://www.astro.caltech.edu/~tjp/pgplot/
pgx parallel graph analytics Computer Science http://www.oracle.com
phantomjs Headless WebKit scriptable with a JavaScript API Internet http://phantomjs.org
photoscan Commercial Photogrammetry software - bring your own license Data Analysis http://www.agistoft.com
php general-purpose scripting language Internet http://php.net
phylocsf determine whether multi-species nucleotide alignment is likely to represent protein-coding region Bioinformatics http://github.com/mlin/PhyloCSF
picard Java-based command-line utilities to manipulate SAM files Bioinformatics http://picard.sourceforge.net
picrust a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes Bioinformatics http://picrust.github.io
pigz parallel implementation of gzip System Tools http://zlib.net/pigz
pin binary instrumentation tool Programming Tools http://software.intel.com/en-us/articles/pintool-downloads
pindel detection of breakpoints of deletions, insertions, inversions, duplications, and other structural variants Bioinformatics http://trac.nbic.nl/pindel
pipipes piRNA pipeline collection developed in Zamore Lab Bioinformatics http://github.com/bowhan/piPipes
pixman a low-level software library for pixel manipulation Libraries http://www.pixman.org
plink whole genome association analysis toolset Bioinformatics http://www.cog-genomics.org/plink2
plumed open source library for free energy calculations Chemistry http://plumed.org
pmw toolkit for building high-level compound widgets in Python using the Tkinter module Libraries http://pmw.sourceforge.net
popbam population-based analyses of next-generation sequencing data Bioinformatics http://sourceforge.net/projects/popbam
popoolation compare allele frequencies for SNPs between two or more populations Bioinformatics http://sourceforge.net/projects/popoolation2
poreseq error correction and variant calling algorithm for nanopore sequencing Bioinformatics http://github.com/tszalay/poreseq
poretools toolkit for working with nanopore sequencing data from Oxford Nanopore Bioinformatics http://poretools.readthedocs.io
praat phonetics by computer Computer Science http://fon.hum.uva.nl/praat
probabel tools for genome-wide association analysis of imputed genetic data Bioinformatics http://genable.org/packages/ProbABEL
progressivecactus multiple genome aligner Bioinformatics https://github.com/glennhickey/progressiveCactus
proovread PacBio hybrid error correction through iteractive short read consensus Bioinformatics http://github.com/BioInf-Wuerzburg/proovread
protobuf language neutral, platform neutral extensible mechanism for serializing structured data Programming Tools http://developers.google.com/protocol-buffers
provide program for viral diversity estimation Bioinformatics http://metagenomics.atc.tcs.com/binning/ProViDE
psfj automatically analyses the full field-of-view (FOV) performance of a given fluorescence microscope/objective lens combination with respect to its optical resolution and chromatic aberrations Graphics http://www.knoplab.de/psfj
psi4conda open-source quantum chemistry Chemistry http://www.psicode.org
pt3 analysis of time-resolved photon counting from PicoHarp 300 T3 mode files Chemistry http://circ.rochester.edu
pybedtools wrapper for BEDTools Bioinformatics http://pypi.python.org/pypi/pybedtools
pycifrw CIF/STAR file support for Python Chemistry http://pypi.python.org/pypi/PyCifRW
pycogent software library for genomic biology Bioinformatics http://pycogent.org
pycuda CUDA wrapper for python Programming Tools http://pypi.python.org/pypi/pycuda
pyfasta fast, memory-efficient, pythonic access to fasta sequence files Bioinformatics http://pypi.python.org/pypi/pyfasta
pymol molecular visualization system on an open-source foundation Graphics http://www.pymol.org
pyqtgraph python graphics and GUI utility Graphics http://pyqtgraph.org
pysam python interface for SAM/BAM sequence alignment and mapping format Bioinformatics http://code.google.com/p/pysam
pysamstats Python utility for calculating statistics against genome positions based on sequence alignments from a SAM or BAM file Bioinformatics http://github.com/alimanfoo/pysamstats
pyslurm Python interface to slurm 15.08.8 Libraries https://github.com/PySlurm
pytables python package for managing hierarchical datasets Libraries http://www.pytables.org
python Python programming language Programming Tools http://www.python.org
python3 Python3 programming language Programming Tools http://www.python.org
pyvcf variant call format reader Bioinformatics http://github.com/jamescasbon/PyVCF
pyxaid PYthon eXtension for Ab Initio Dynamics Chemistry http://www.acsu.buffalo.edu/~alexeyak/pyxaid/overview.html
qctool quality control and analysis of gwas datasets Bioinformatics http://www.well.ox.ac.uk/~gav/qctool
qdmr quantitative differentially methylated region Bioinformatics http://bioinfo.hrbmu.edu.cn/qdmr
qe electronic-structure calculations Chemistry http://www.quantum-espresso.org
qgis geographic information system Libraries http://qgis.org
qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthest-site Delaunay triangulation, and furthest-site Voronoi diagram Mathematics http://www.qhull.org
qiime Quantitative Insights into Microbial Ecology Molecular Biology http://qiime.org
qiimetomaaslin convert Qiime output to MaAsLin input Bioinformatics http://bitbucket.org/biobakery/qiimetomaaslin
qrupdate Fortran library for fast updates of QR and Cholesky decompositions. Libraries http://sourceforge.net/projects/qrupdate
qt cross-platform application and UI framework for developers using C++ or QML Libraries http://qt-project.org
qtwebkit Qt port of WebKit Libraries http://trac.webkit.org/wiki/QtWebKit
quast QUality ASessment Tool for Genome Assemblies Bioinformatics http://github.com/ablab/quast
r free software environment for statistical computing and graphics Data Analysis http://www.r-project.org
raxml randomized axelerated maximum likelihood Bioinformatics http://sco.h-its.org/exelixis/web/software/raxml
readline readline utility Libraries http://www.gnu.org
realpath list contents of directories in a tree-like format System Tools http://linux.die.net/man/1/realpath
recon de novo algorithm for identification of repeat families from biological sequences Bioinformatics http://www.genetics.wustl.edu/eddy/recon
repdenovo construct repeats directly from raw reads Bioinformatics http://github.com/Reedwarbler/REPdenovo
repeatmasker program that screens DNA sequences for interspersed repeats and low complexity DNA sequences Bioinformatics http://www.repeatmasker.org
repeatmodeler RepeatModeler is a de-novo repeat family identification and modeling package Bioinformatics http://repeatmasker.org
resqc RNA-seq quality control package Bioinformatics http://rseqc.sourceforge.net
retroseq discovery and genotyping of transposable element variants Bioinformatics http://github.com/tk2/RetroSeq/releases
rh6 RHEL6 packages System Tools http://redhat.com
rmagick Ruby+ImageMagick Libraries http://rmagick.github.io
rmats multivariate analysis of transcript splicing Bioinformatics http://rnaseq-mats.sourceforge.net
rmblast RepeatMasker compatible version of the standard NCBI BLAST suite Bioinformatics http://www.repeatmasker.org/RMBlast.html
rna-star spliced transcripts alignment to a reference Bioinformatics http://code.google.com/p/rna-star
rnastructure RNA and DNA secondary structure prediction and analysis Bioinformatics http://rna.urmc.rochester.edu/RNAstructure.html
rodeo A native Python IDE for Data Science Data Analysis http://rodeo.yhat.com
root data analysis framework Data Analysis http://root.cern.ch
rsem RNA-Seq by expectation maximization Bioinformatics http://dewlab.biostat.wisc.edu/rsem
rstudio GUI for R Data Analysis http://rstudio.com
ruby dynamic, open source programming language with a focus on simplicity and productivity Programming Tools http://ruby-lang.org
sage open-source mathematics software system Mathematics http://sagemath.org
salmon highly accurate and wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments Bioinformatics http://github.com/COMBINE-lab/salmon
samstat displays various properties of next-generation sequencing reads stored in SAM/BAM format Bioinformatics http://sourceforge.net/projects/samstat
samtools utilities for sequence alignments Bioinformatics http://samtools.sourceforge.net
sas data management Data Analysis http://www.sas.com
sbt an open source build tool for Scala and Java projects, similar to Javas Maven or Ant. Programming Tools http://www.scala-sbt.org
scala an object-functional programming and scripting language for general software applications Programming Tools http://www.scala-lang.org
scarpa stand-alone scaffolding tool for NGS data Bioinformatics http://compbio.cs.toronto.edu/hapsembler/scarpa.html
schrodinger computational chemistry package Chemistry http://schrodinger.com
scilab numerical computation Mathematics http://www.scilab.org
scipy open source library of scientific tools Libraries http://scipy.org
scons software construction tool Programming Tools http://www.scons.org
screen window manager Accessories http://gnu.org
sendemail sending SMTP mail from command line System Tools http://caspian.dotconf.net/menu/Software/SendEmail
seqclean sequence cleaner Bioinformatics http://seqclean.sourceforge.net
seqtk toolkit for processing sequences in FASTA/Q formats Bioinformatics http://github.com/lh3/seqtk
sga string graph assembler Bioinformatics http://github.com/jts/sga
shapeit estimation of haplotypes Bioinformatics http://mathgen.stats.ox.ac.uk/genetic_software/shapeit/shapeit.html
shm a powerful seismic waveform analysis tool Physics http://www-seismic-handler.org
shrimp SHort Read Mapping Package Bioinformatics http://compbio.cs.toronto.edu/shrimp
siesta electronic structure calculations Chemistry http://www.icmab.es/siesta
slicer visualization and medical image computing Graphics http://slicer.org
slurm Slurm job scheduler System Tools http://slurm.schedmd.com/
smartgit SmartGit is a Git client with Mercurial and Subversion support. SmartGit is free for non-commercial use and runs on Mac OS X, Windows and Linux. Programming Tools http://www.syntevo.com/smartgit/
snappy fast compressor/decompressor System Tools http://github.com/google/snappy
snptest analysis of single SNP association Bioinformatics http://mathgen.stats.ox.ac.uk/genetics_software/snptest/snptest.html
soapdenovo a short read de novo assembly tool, is a package for assembling short oligonucleotide into contigs and scaffolds Libraries http://soap.genomics.org.cn/index.html
sopra assembler for mate pair/paired-end reads from high throughput sequencing platforms, e.g. Illumina and SOLiD Bioinformatics http://www.physics.rutgers.edu/~anirvans/SOPRA
sourcetracker Bayesian approach to estimating proportion of a novel community from a set of source environments Bioinformatics http://sourceforge.net/projects/sourcetracker
soxr resampler library Libraries http://sourceforge.net/p/soxr
spades genome assembler Bioinformatics http://bioinf.spbau.ru/spades
sparc sparsity-based consensus algorithm for long erroneous sequencing reads Bioinformatics http://github.com/yechengxi/Sparc
spark a fast and general-purpose cluster computing system System Tools http://spark.apache.org
sparsehash extremely memory-efficient hash_map implementation Programming Tools http://code.google.com/p/sparsehash
sphinx tool that makes it easy to create intelligent and beautiful documentation Libraries http://sphinx-doc.org
splicegrapher prediction of alternative splicing patterns Bioinformatics http://sourceforge.net/projects/splicegrapher
sqlcipher database encryption for SQLite Data Analysis http://sqlcipher.net
sqlite SQL database engine Data Analysis http://www.sqlite.org
sqliteman sqlite3 admin tool Data Analysis http://sourceforge.net/projects/sqliteman
sqliteodbc odbc wrapper for sqlite Data Analysis http://www.ch-werner.de/sqliteodbc
sratoolkit access data from sequence read archive Bioinformatics http://www.ncbi.nlm.nih.gov/books/NBK158900
stack Haskell tool stack Programming Tools http://haskellstack.org
stampy mapping of short reads onto a reference genome Bioinformatics http://www.well.ox.ac.uk/project-stampy
stata data analysis and statistics Data Analysis http://www.stata.com
stride integrates string and de Bruijn graph by decomposing reads within error-prone regions Bioinformatics http://github.com/ythuang0522/StriDe
stringtie transcript assembly and quantification for RNA-seq Bioinformatics http://ccb.jhu.edu/software/stringtie
subversion open source version control system Programming Tools http://subversion.apache.org
suitesparse suite of sparse matrix algorithms Libraries http://www.cise.ufl.edu/research/sparse/SuiteSparse/
sundials suite of nonlinear and differential/algebraic equation solvers Mathematics http://computation.llnl.gov/projects/sundials-suite-nonlinear-differential-algebraic-equation-solvers/sundials-software
swig interface compiler Programming Tools http://www.swig.org
tabix utilities for SAMtools Bioinformatics http://sourceforge.net/projects/samtools/files/tabix
tandem X! Tandem spectrum modeler Chemistry http://www.thegpm.org/tandem
tar create archives System Tools http://www.gnu.org/software/tar
tcl Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language Programming Tools http://www.tcl.tk/
tclap templatized C++ command line parser Programming Tools http://sourceforge.net/projects/tclap
tcllib The Tcl Library is a kitchen sink of packages across a broad spectrum of things Libraries http://core.tcl.tk/tcllib/home
temp detecting transposable elements, insertions and absences from pooled high-throughput sequencing data Bioinformatics http://github.com/JialiUMassWengLab/TEMP
texinfo official documentation format of the GNU project System Tools http://www.gnu.org/software/texinfo/
texlive TeX document production system Accessories https://www.tug.org/texlive/
tiff TIFF Library and Utilities Libraries http://www.remotesensing.org/libtiff/
tinker molecular mechanics and dynamics with special features for biopolymers Molecular Biology http://dasher.wustl.edu/tinker
tk Tk is a graphical user interface toolkit that takes developing desktop applications to a higher level than conventional approaches Programming Tools http://www.tcl.tk/
tmux terminal multiplexer System Tools https://tmux.github.io
tophat fast splice junction mapper for RNA-Seq reads Bioinformatics http://tophat.cbcb.umd.edu
torch scientific computing framework for luajit Programming Tools https://github.com/torch
toyz Toyz for Data Analysis and Reduction Data Analysis https://github.com/fred3m/toyz
transdecoder find coding regions within transcripts Bioinformatics http://transdecoder.github.io
tree list contents of directories in a tree-like format System Tools http://linux.die.net/man/1/tree
trf Tandem Repeats Finder Bioinformatics http://tandem.bu.edu/trf/trf.html
trimgalore quality and adaptor trimming for RRBS or standard FastQ files Bioinformatics http://www.bioinformatics.babraham.ac.uk
trimmomatic flexible read trimming tool for Illumina NGS data Bioinformatics http://www.usadellab.org/cms/index.php?page=trimmomatic
trinityrnaseq RNA-seq de novo assembly Bioinformatics http://trinityrnaseq.sourceforge.net
turbovnc offshoot of TightVNC that accelerates the Tight and JPEG encoding paths of the latter, in part by taking advantage of libjpeg-turbo, a SIMD-accelerated version of libjpeg System Tools http://sourceforge.net/projects/virtualgl/files/TurboVNC
ucsc genome browser command-line tools Bioinformatics http://genome.ucsc.edu
unicycler hybrid assembly pipeline for bacterial genomes Bioinformatics http://github.com/rrwick/Unicycler
unison file synchronization System Tools http://www.cis.upenn.edu/~bcpierce/unison
unixodbc open specification for data sources Data Analysis http://www.unixodbc.org
unrar archive manager System Tools http://www.rarlab.com
unzip ZIP extraction Accessories http://www.linuxfromscratch.org/blfs/view/svn/general/unzip.html
valgrind debugging and profiling Programming Tools http://valgrind.org
vardict sensitive variant called for both single and paired sample variant calling from BAM files Bioinformatics http://github.com/AstraZeneca-NGS/VarDict
varianttools software tool for the manipulation, annotation, selection, simulation, and analysis of variants in the context of next-gen sequencing analysis Bioinformatics http://github.com/vatlab/VariantTools
varscan variant detection in next-generation sequencing data Bioinformatics http://sourceforge.net/projects/varscan
vcflib simple C++ library for parsing and manipulating VCF files Bioinformatics http://github.com/ekg/vcflib
vcftools package for working with VCF files Bioinformatics http://vcftools.sourceforge.net
velvet sequence assembler for very short reads Bioinformatics http://www.ebi.ac.uk/~zerbino/velvet
velvetoptimiser Perl script for automatically optimizing the three primary parameter optinos for the velvet de novo sequence assembler Bioinformatics http://bioinformatics.net.au/software.velvetoptimiser.shtml
vicare implementation of Scheme language compliant with R6RS standard with several language extensions Programming Tools http://marcomaggi.github.io/vicare.html
vienna prediction and comparison of RNA secondary structures Bioinformatics http://www.tbi.univie.ac.at/RNA
virtualgl OpenGL interposer that allows applications to use remote display hardware Libraries http://www.virtualgl.org
virusseq detection of known viruses and integration sites Bioinformatics http://odin.mdacc.tmc.edu/~xsu1/VirusSeq.html
visit Open Source, interactive, scalable, visualization, animation and analysis tool Graphics https://wci.llnl.gov/codes/visit/
visualsfm GUI application for 3D reconstruction using structure from motion Graphics http://ccwu.me/vsfm
vmd visual molecular dynamics Graphics http://www.ks.uiuc.edu/Research/vmd
volview open-source, intuitive, interactive system for volume visualization that allows researchers to quickly explore and analyze complex 3D medical or scientific data Graphics http://www.kitware.com/opensource/volview.html
voro Voronoi diagram Mathematics http://math.lbl.gov/voro++
vpnc virtual private network consortium Internet http://vpnc.org
vtk visualization toolkit Graphics http://vtk.org
vxl collection of C++ libraries designed for computer vision research and implementation Libraries http://vxl.sourceforge.net
wannier90 maximally-localized Wannier functions Chemistry http://www.wannier.org
weblogo create sequence logos Bioinformatics http://weblogo.berkeley.edu
weka machine learning algorithms for data mining Data Analysis http://www.cs.waikato.ml/ml/weka
westpa The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis Molecular Biology http://westpa.github.io
wgs whole-genome shotgun assembler Bioinformatics http://sourceforge.net/projects/wgs-assembler
wine compatibility layer for Windows apps - 32 bit System Tools http://winehq.org
wx cross-platform GUI library Libraries http://www.wxwidgets.org
wxPython a blending of the wxWidgets C++ class library with the Python programming language Libraries http://www.wxpython.org
wxwidgets cross-platform GUI library Programming Tools http://wxwidgets.org
x-devel X windows devel pkgs Libraries http://www.x.org
xblas eXtended precision Basic Linear Algebra Subroutines Libraries http://www.netlib.org/xblas
xcb X protocol C-language Binding (XCB) Libraries http://xcb.freedesktop.org
xcrysden X-window CRYstalline Structures and DENsities Chemistry http://www.xcrysden.org
xdmf Extensible Data Module and Format, a data model, library and file format for storing and managing data Libraries http://xdmf.org/index.php/Main_Page
xerces-c XML parser Programming Tools http://xerces.apache.org
xls2csv converts xsl files to csv - perl version System Tools http://search.cpan.org/~ken/xls2csv-1.07/script/xls2csv
xpdf PDF viewer Accessories http://www.foolabs.com/xpdf
xterm Xwindow terminal System Tools http://invisible-island.net/xterm
xz free general-purpose data compression software with high compression ratio Libraries http://tukaani.org/xz/
yaehmop Yet Another extended Huckel Molecular Orbital Package Chemistry http://yaehmop.sourceforge.net
yasm Yasm assembler Programming Tools http://yasm.tortall.net
zlib Compression Library Libraries http://zlib.net
zmq ZeroMQ lightweight messaging kernel Libraries https://github.com/zeromq/libzmq